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H2AX H2A.X variant histone [ Homo sapiens (human) ]

Gene ID: 3014, updated on 5-Jan-2025

Summary

Official Symbol
H2AXprovided by HGNC
Official Full Name
H2A.X variant histoneprovided by HGNC
Primary source
HGNC:HGNC:4739
See related
Ensembl:ENSG00000188486 MIM:601772; AllianceGenome:HGNC:4739
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
H2A.X; H2A/X; H2AFX
Summary
Histones are basic nuclear proteins that are responsible for the nucleosome structure of the chromosomal fiber in eukaryotes. Two molecules of each of the four core histones (H2A, H2B, H3, and H4) form an octamer, around which approximately 146 bp of DNA is wrapped in repeating units, called nucleosomes. The linker histone, H1, interacts with linker DNA between nucleosomes and functions in the compaction of chromatin into higher order structures. This gene encodes a replication-independent histone that is a member of the histone H2A family, and generates two transcripts through the use of the conserved stem-loop termination motif, and the polyA addition motif. [provided by RefSeq, Oct 2015]
Orthologs
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Genomic context

See H2AX in Genome Data Viewer
Location:
11q23.3
Exon count:
1
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (119093874..119095465, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (119114257..119115848, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (118964584..118966175, complement)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5619 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5620 Neighboring gene VPS11 core subunit of CORVET and HOPS complexes Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:118955192-118955889 Neighboring gene hydroxymethylbilane synthase Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:118963458-118963970 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:118965105-118965668 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:118965669-118966232 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:118966233-118966796 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:118966797-118967358 Neighboring gene dolichyl-phosphate N-acetylglucosaminephosphotransferase 1 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr11:118972216-118973415 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3968 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3969 Neighboring gene C2CD2 like Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3970 Neighboring gene histone H4 transcription factor

Genomic regions, transcripts, and products

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
Tat tat HIV-1 Tat peptides bind core histones H2A, H2B, H3 and H4, and Tat protein recruits histone acetyltransferases to the HIV-1 LTR promoter leading to acetylation of histones H3 and H4, derepressing chromatin structure and increasing NFkappaB responsiveness PubMed
Vpr vpr Soluble HIV-1 Vpr induces a DNA damage response by forming H2AX- and 53BP1-containing DNA repair foci PubMed
vpr HIV-1 Vpr expression in HeLa cells and human primary CD4+ lymphocytes induces phosphorylation of H2AFX and formation of nuclear foci containing H2AFX and BRCA1 PubMed
vpr Recruitment of a catalytically active CRL4A (VPRBP) complex is required to observe HIV-1 Vpr-interacting unknown cellular ubiquitinated proteins. Phosphorylation of H2AX requires Vpr-induced K48 residue polyubiquitination PubMed
vpr HIV-1 Vpr binds DCAF1 and activates the DNA damage response in renal tubule epithelial cells, in which gamma H2AX-positive nuclei are abundant compared to the control PubMed
integrase gag-pol HIV-1 IN-mediated proviral DNA integration triggers cell death during HIV-1 infection. The mechanism of killing during viral integration involves activation of DNA-PK, which causes phosphorylation of p53 and histone gammaH2AX PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

Interactions

General gene information

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA binding PubMed 
enables chromatin-protein adaptor activity PubMed 
enables damaged DNA binding  
enables enzyme binding PubMed 
enables histone binding PubMed 
enables protein binding PubMed 
enables protein heterodimerization activity  
enables structural constituent of chromatin  
Process Evidence Code Pubs
involved_in DNA damage checkpoint signaling PubMed 
involved_in DNA damage response  
involved_in DNA damage response PubMed 
involved_in DNA damage response PubMed 
involved_in cellular response to gamma radiation  
involved_in cellular senescence  
involved_in cerebral cortex development  
involved_in double-strand break repair PubMed 
involved_in double-strand break repair via homologous recombination  
involved_in heterochromatin formation  
involved_in meiotic cell cycle  
involved_in nucleosome assembly PubMed 
involved_in positive regulation of DNA repair PubMed 
involved_in protein localization to site of double-strand break PubMed 
involved_in response to ionizing radiation PubMed 
involved_in spermatogenesis  
Component Evidence Code Pubs
located_in XY body  
located_in centrosome PubMed 
colocalizes_with chromosome, telomeric region PubMed 
located_in condensed nuclear chromosome  
located_in extracellular exosome PubMed 
located_in male germ cell nucleus  
located_in nuclear speck  
located_in nucleoplasm  
located_in nucleoplasm  
part_of nucleosome  
located_in nucleus PubMed 
is_active_in nucleus  
located_in nucleus PubMed 
located_in nucleus PubMed 
located_in replication fork  
located_in site of DNA damage PubMed 
is_active_in site of double-strand break PubMed 
located_in site of double-strand break PubMed 

General protein information

Preferred Names
histone H2AX
Names
H2A histone family member X
H2AX histone
histone H2A.x

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_002105.3NP_002096.1  histone H2AX

    See identical proteins and their annotated locations for NP_002096.1

    Status: REVIEWED

    Source sequence(s)
    AP003391
    Consensus CDS
    CCDS8410.1
    UniProtKB/Swiss-Prot
    P16104, Q4ZGJ7, Q6IAS5
    UniProtKB/TrEMBL
    B2R5B3
    Related
    ENSP00000434024.1, ENST00000530167.2
    Conserved Domains (1) summary
    PTZ00017
    Location:1131
    PTZ00017; histone H2A; Provisional

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    119093874..119095465 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    119114257..119115848 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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